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Misra R, Maity A, Kundu S, Bhunia M, Nanda B, Maiti NC, Pal U. Loop Dynamics and Conformational Flexibility in Dengue Serine Protease Activity: Noninvasive Perturbation by Solvent Exchange. J Chem Inf Model 2023; 63:2122-2132. [PMID: 36943246 DOI: 10.1021/acs.jcim.2c01349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Molecular mechanics play an important role in enzyme action and understanding the dynamics of loop motion is key for designing inhibitors of an enzyme, particularly targeting the allosteric sites. For the successful creation of new protease inhibitors targeting the dengue serine protease, our current investigation detailed the intricate structural dynamics of NS2B/NS3 dengue protease. This enzyme is one of the most essential enzymes in the life cycle of the dengue virus, which is responsible for the activation/processing of viral polyprotein, thus making it a potential target for drug discovery. We showed that the internal dynamics of two regions, fingers 1 and 2 (R24-G39 and L149-A164, respectively) adjacent to the active site triad of this protease, control the enzyme action. Each of these regions is composed of two antiparallel β-strands connected by β-turn/hairpin loops. The correlated bending and rocking motions in the two β-turns on either side of the active site were found to modulate the activity of the enzyme to a large extent. With increasing concentration of cosolvent dimethyl sulfoxide, correlated motions in the finger 2 region get diminished and bending of finger 1 increases, which are also reflected in the loss of enzyme activity. Decreasing temperature and mutations in neighboring nonsubstrate binding residues show similar effects on loop motion and enzyme kinetics. Therefore, in vitro noninvasive perturbation of these motions by the solvent exchange as well as cold stress in combination with in silico molecular dynamics simulations established the importance of the two β-turns in the functioning of dengue virus serotype 2 NS2B/NS3 serine protease.
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Affiliation(s)
- Rajdip Misra
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Anupam Maity
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Shubham Kundu
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Mrinmay Bhunia
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Banadipa Nanda
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Nakul C Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Uttam Pal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
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Checkerboard arranged G4 nanostructure-supported electrochemical platform and its application to unique bio-enzymes examination. Bioelectrochemistry 2023; 149:108282. [DOI: 10.1016/j.bioelechem.2022.108282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022]
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Wang F, Du H, Li B, Luo Z, Zhu L. Unlocking phenotypic plasticity provides novel insights for immunity and personalized therapy in lung adenocarcinoma. Front Genet 2022; 13:941567. [PMID: 36147496 PMCID: PMC9486167 DOI: 10.3389/fgene.2022.941567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Unlocking phenotype plasticity (UPP) has been shown to have an essential role in the mechanism of tumor development and therapeutic response. However, the clinical significance of unlocking phenotypic plasticity in patients with lung adenocarcinoma is unclear. This study aimed to explore the roles of unlocking phenotypic plasticity in immune status, prognosis, and treatment in patients with lung adenocarcinoma (LUAD). Methods: Differentially expressed genes (DEGs) and clinical information of UPP were selected from the cancer genome atlas (TCGA) database, and the GO, KEGG enrichment analyses were performed. The independent prognostic genes were determined by univariate and multivariate Cox regression, and the UPP signature score was constructed. Patients with LUAD were divided into high- and low-risk groups according to the median of score, and the immunocytes and immune function, the gene mutation, and drug sensitivities between the two groups were analyzed. Finally, the results were validated in the GEO database. Results: Thirty-nine significantly DEGs were determined. Enrichment analysis showed that UPP-related genes were related to protein polysaccharides and drug resistance. The prognostic results showed that the survival of patients in the high-risk group was poorer than that in the low-risk group (p < 0.001). In the high- and low-risk groups, single nucleotide polymorphism (SNP) and C > T are the most common dissent mutations. The contents of immune cells were significantly different between high- and low-risk groups. And the immune functions were also significantly different, indicating that UPP affects the immunity in LUAD. The results from TCGA were validated in the GEO. Conclusion: Our research has proposed a new and reliable prognosis indicator to predict the overall survival. Evaluation of the UPP could help the clinician to predict therapeutic responses and make individualized treatment plans in patients with LUAD.
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Affiliation(s)
- Feng Wang
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Hongjuan Du
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Bibo Li
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Zhibin Luo
- Department of Oncology, Chongqing General Hospital, Chongqing, China
| | - Lei Zhu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Lei Zhu,
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